AMBER Archive (2004)

Subject: Re: AMBER: average structure using ptraj

From: Chris Moth (
Date: Fri Jul 02 2004 - 12:11:42 CDT

Quoting NI AI <aini_at_UMDNJ.EDU>:

> Dear Dr. Cheatham,
> Thank you very much for your answer! I striped water and counter ions and
> used modified script. The minimization went through. However, this
> minimization is done in vaccum since I don't know how to put water and ions
> back to the system. Do I need to read in average.pdb to xleap and prepare
> another .top and .crd file for minimization? or you have different way to do
> that?

My experience with average structures is limited to preparation of several
presentation graphics to describe key interactions in a ligand/protein complex I
am working on.

For this work, minimization of average.pdb, simply and quickly in vacuum, by
creating a new .top and .crd worked out fine (protons had normal positions, bond
lengths, etc). Of course, you'll want to look at what you get :)

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